Dear Hervé,
Is it possible to ignore minoverlap when people set maxgap greater than 0
and give a message for that?
Yours sincerely,
Jianhong Ou
LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605
On 7/23/13 5:35 PM, "Hervé Pagès" <hpa...@fhcrc.org> wrote:
>Hi,
>
>This fails in Bioc-devel only and the following fix "seems" to address
>the problem:
>
> hpages@thinkpad:~/svn/bioconductor/Rpacks/IRanges$ svn diff
>R/findOverlaps-methods.R
> Index: R/findOverlaps-methods.R
> ===================================================================
> --- R/findOverlaps-methods.R (revision 78801)
> +++ R/findOverlaps-methods.R (working copy)
> @@ -142,7 +142,7 @@
> # preprocess query
> preprocRes <- .preProcess_findOverlaps_query(query,
>maxgap, minoverlap)
> origQuery <- preprocRes$origQuery
> - unsortedQuery <- preprocRes$origQuery
> + unsortedQuery <- preprocRes$unsortedQuery
> query <- preprocRes$query
> query_ord <- preprocRes$query_ord
>
>However a *real* fix would be to actually clarify what's the meaning of
>using 'maxgap' and 'minoverlap' together. Right now the result below
>doesn't make much sense to me (using Bioc-release):
>
> > findOverlaps(IRanges(1, 5), IRanges(7, 10), maxgap=3, minoverlap=2)
> Hits of length 0
> queryLength: 1
> subjectLength: 1
>
> > findOverlaps(IRanges(1, 5), IRanges(7, 10), maxgap=4, minoverlap=2)
> Hits of length 1
> queryLength: 1
> subjectLength: 1
> queryHits subjectHits
> <integer> <integer>
> 1 1 1
>
>H.
>
>
>On 07/23/2013 12:08 PM, Maintainer wrote:
>> Hi,
>>
>> I got "negative widths are not allowed" error when I use findOverlaps.
>> Could anybody help me to figure this out? Thanks. Here is the code:
>>
>> > library("IRanges")
>> Loading required package: BiocGenerics
>> Loading required package: parallel
>>
>> Attaching package: ŒBiocGenerics¹
>>
>> The following objects are masked from Œpackage:parallel¹:
>>
>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>> clusterExport, clusterMap, parApply, parCapply, parLapply,
>> parLapplyLB, parRapply, parSapply, parSapplyLB
>>
>> The following object is masked from Œpackage:stats¹:
>>
>> xtabs
>>
>> The following objects are masked from Œpackage:base¹:
>>
>> anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
>> duplicated, eval, Filter, Find, get, intersect, lapply, Map,
>> mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>> Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff,
>> sort, table, tapply, union, unique, unlist
>>
>> > Ranges1 <- sort(IRanges(start=c(3123260, 167889600), end=c(3123360,
>> 167893599), names=c("Site5", "Site12")))
>> > Ranges2 <- sort(IRanges(start=c(312326, 3123260, 167888600),
>> end=c(312586, 3123470, 167888999), names=c("t11", "t5", "t17")))
>> > tree = IntervalTree(Ranges2)
>> > findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20,
>> select = "first")
>> Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE =
>> "IRanges") :
>> solving row 2: negative widths are not allowed
>> > traceback()
>> 11: .Call(.NAME, ..., PACKAGE = PACKAGE)
>> 10: .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
>> 9: solveUserSEW0(start = start, end = end, width = width)
>> 8: IRanges(pmax.int(qstart, sstart), pmin.int(send, qend))
>> 7: .local(x, ...)
>> 6: ranges(result, unsortedQuery, subject)
>> 5: ranges(result, unsortedQuery, subject)
>> 4: .postProcess_findOverlaps_result(result, unsortedQuery, origQuery,
>> subject, type, minoverlap, maxgap, origSelect)
>> 3: .local(query, subject, maxgap, minoverlap, type, select, ...)
>> 2: findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20,
>> select = "first")
>> 1: findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20,
>> select = "first")
>> > sessionInfo()
>> R Under development (unstable) (2013-04-30 r62697)
>> Platform: x86_64-apple-darwin12.3.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] parallel stats graphics grDevices utils datasets methods
>> [8] base
>>
>> other attached packages:
>> [1] IRanges_1.19.19 BiocGenerics_0.7.3
>>
>> loaded via a namespace (and not attached):
>> [1] stats4_3.1.0
>>
>>
>> Yours sincerely,
>>
>> Jianhong Ou
>>
>> LRB 670A
>> Program in Gene Function and Expression
>> 364 Plantation Street Worcester,
>> MA 01605
>>
>>
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>
>--
>Hervé Pagès
>
>Program in Computational Biology
>Division of Public Health Sciences
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N, M1-B514
>P.O. Box 19024
>Seattle, WA 98109-1024
>
>E-mail: hpa...@fhcrc.org
>Phone: (206) 667-5791
>Fax: (206) 667-1319
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